AMBER Archive (2008)

Subject: AMBER: MM-GBSA with very positive GB value

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Fri Jun 13 2008 - 02:05:02 CDT

Dear Sir/Madam,
 
I did a MM-GBSA calculation for a short polymer, however, I found the following results very strange that GB is a positive value. I am trying to interpret the result as the polymer is hydrophobic (as indicated by the large negative VDW value) in nature, so it is not soluble in water. Thus, a positive (unfavor) solvation energy (GB) is obtained. Could anyone cold like comment on this if I have interpret that data correctly or I must have done something wrong in the calculation?
 
Best regards and many thanks,
 
Cat.
 

ELE
-6.3

VDW
-46.48

INT
-0.01

GAS
-52.8

GBSUR
-2.89

GB
24.89

GBSOL
22

GBELE
18.59

GBTOT
-30.79

TSTRA
-12.92

TSROT
-10.76

TSVIB
5.83

TSTOT

-17.85

 
Thus,
 
VDW+GBSUR

 
 
 
-49.37

ELE+GB
18.59

GBTOT-TSTOT
-12.94
_________________________________________________________________
Discover the new Windows Vista
http://search.msn.com/results.aspx?q=windows+vista&mkt=en-US&form=QBRE
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu